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comparison picard_QualityScoreDistribution.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>chart quality score distribution</description> 2 <description>chart quality score distribution</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="3.4.1">r-base</requirement>
9 </expand> 8 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 @java_options@ 10 @java_options@
12 ##set up input files 11 ##set up input files
13 @symlink_element_identifier@ 12 @symlink_element_identifier@
14 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
15 14
16 @handle_reference_source@ 15 @handle_reference_source@
17 16
18 picard 17 picard QualityScoreDistribution
19 QualityScoreDistribution 18 --INPUT '$escaped_element_identifier'
20 INPUT='$escaped_element_identifier' 19 --OUTPUT '${outFile}'
21 OUTPUT="${outFile}" 20 --CHART_OUTPUT '${pdfFile}'
22 CHART_OUTPUT="${pdfFile}" 21 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
23 REFERENCE_SEQUENCE="${reference_fasta_filename}" 22 --ALIGNED_READS_ONLY '${aligned_reads_only}'
24 ALIGNED_READS_ONLY="${aligned_reads_only}" 23 --PF_READS_ONLY '${pf_reads_only}'
25 PF_READS_ONLY="${pf_reads_only}" 24 --INCLUDE_NO_CALLS '${include_no_calls}'
26 INCLUDE_NO_CALLS="${include_no_calls}"
27 25
28 ASSUME_SORTED="${assume_sorted}" 26 --ASSUME_SORTED '${assume_sorted}'
29 27
30 VALIDATION_STRINGENCY="${validation_stringency}" 28 --VALIDATION_STRINGENCY '${validation_stringency}'
31 QUIET=true 29 --QUIET true
32 VERBOSITY=ERROR 30 --VERBOSITY ERROR
33 31
34 ]]></command> 32 ]]></command>
35 <inputs> 33 <inputs>
36 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 34 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
37 <conditional name="reference_source"> 35 <conditional name="reference_source">
38 <param name="reference_source_selector" type="select" label="Load reference genome from"> 36 <param name="reference_source_selector" type="select" label="Load reference genome from">
39 <option value="cached">Local cache</option> 37 <option value="cached">Local cache</option>
40 <option value="history">History</option> 38 <option value="history">History</option>
41 </param> 39 </param>
42 <when value="cached"> 40 <when value="cached">
43 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> 41 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
44 <options from_data_table="all_fasta"> 42 <options from_data_table="all_fasta">
45 </options> 43 </options>
46 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
47 </param> 45 </param>
48 </when> 46 </when>
49 <when value="history"> 47 <when value="history">
50 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> 48 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
51 </when> 49 </when>
52 </conditional> 50 </conditional>
53 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> 51 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
54 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> 52 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
55 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/> 53 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
56 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> 54 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
57 55 <expand macro="VS"/>
58 <expand macro="VS" /> 56 </inputs>
59 57 <outputs>
60 </inputs> 58 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
61 59 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
62 <outputs> 60 </outputs>
63 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 61 <tests>
64 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 62 <test>
65 </outputs> 63 <param name="assume_sorted" value="true"/>
66 64 <param name="aligned_reads_only" value="false"/>
67 <tests> 65 <param name="pf_reads_only" value="false"/>
68 <test> 66 <param name="include_no_calls" value="false"/>
69 <param name="assume_sorted" value="true" /> 67 <param name="reference_source_selector" value="history"/>
70 <param name="aligned_reads_only" value="false" /> 68 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa"/>
71 <param name="pf_reads_only" value="false" /> 69 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam"/>
72 <param name="include_no_calls" value="false" /> 70 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
73 <param name="reference_source_selector" value="history" /> 71 </test>
74 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" /> 72 </tests>
75 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" /> 73 <help>
76 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
77 </test>
78 </tests>
79
80
81 <help>
82 74
83 .. class:: infomark 75 .. class:: infomark
84 76
85 **Purpose** 77 **Purpose**
86 78
103 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True 95 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
104 96
105 @more_info@ 97 @more_info@
106 98
107 </help> 99 </help>
108 <expand macro="citations" /> 100 <expand macro="citations"/>
109 </tool> 101 </tool>